Dimension reduction plot tool for colData

Plot results of reduced dimensions data and colors by annotation data stored in the colData slot.

plotSCEDimReduceColData(
  inSCE,
  colorBy,
  reducedDimName,
  sample = NULL,
  groupBy = NULL,
  conditionClass = NULL,
  shape = NULL,
  xlab = NULL,
  ylab = NULL,
  baseSize = 12,
  axisSize = NULL,
  axisLabelSize = NULL,
  dim1 = NULL,
  dim2 = NULL,
  bin = NULL,
  binLabel = NULL,
  dotSize = 0.1,
  transparency = 1,
  colorScale = NULL,
  colorLow = "white",
  colorMid = "gray",
  colorHigh = "blue",
  defaultTheme = TRUE,
  title = NULL,
  titleSize = 15,
  labelClusters = TRUE,
  clusterLabelSize = 3.5,
  legendTitle = NULL,
  legendTitleSize = NULL,
  legendSize = NULL,
  combinePlot = "none",
  plotLabels = NULL
)

Arguments

inSCE

Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.

colorBy

Color by a condition(any column of the annotation data). Required.

reducedDimName

Saved dimension reduction matrix name in the SingleCellExperiment object. Required.

sample

Character vector. Indicates which sample each cell belongs to.

groupBy

Group by a condition(any column of the annotation data). Default NULL.

conditionClass

Class of the annotation data used in colorBy. Options are NULL, "factor" or "numeric". If NULL, class will default to the original class. Default NULL.

shape

Add shapes to each condition.

xlab

Character vector. Label for x-axis. Default NULL.

ylab

Character vector. Label for y-axis. Default NULL.

baseSize

The base font size for all text. Default 12. Can be overwritten by titleSize, axisSize, and axisLabelSize, legendSize, legendTitleSize.

axisSize

Size of x/y-axis ticks. Default NULL.

axisLabelSize

Size of x/y-axis labels. Default NULL.

dim1

1st dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

dim2

2nd dimension to be used for plotting. Can either be a string which specifies the name of the dimension to be plotted from reducedDims, or a numeric value which specifies the index of the dimension to be plotted. Default is NULL.

bin

Numeric vector. If single value, will divide the numeric values into the `bin` groups. If more than one value, will bin numeric values using values as a cut point.

binLabel

Character vector. Labels for the bins created by the `bin` parameter. Default NULL.

dotSize

Size of dots. Default 0.1.

transparency

Transparency of the dots, values will be 0-1. Default 1.

colorScale

Vector. Needs to be same length as the number of unique levels of colorBy. Will be used only if conditionClass = "factor" or "character". Default NULL.

colorLow

Character. A color available from `colors()`. The color will be used to signify the lowest values on the scale. Default 'white'.

colorMid

Character. A color available from `colors()`. The color will be used to signify the midpoint on the scale. Default 'gray'.

colorHigh

Character. A color available from `colors()`. The color will be used to signify the highest values on the scale. Default 'blue'.

defaultTheme

adds grid to plot when TRUE. Default TRUE.

title

Title of plot. Default NULL.

titleSize

Size of title of plot. Default 15.

labelClusters

Logical. Whether the cluster labels are plotted.

clusterLabelSize

Numeric. Determines the size of cluster label when `labelClusters` is set to TRUE. Default 3.5.

legendTitle

title of legend. Default NULL.

legendTitleSize

size of legend title. Default 12.

legendSize

size of legend. Default NULL. Default FALSE.

combinePlot

Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object, while "sample" will output a list of plots separated by sample. Default "none".

plotLabels

labels to each plot. If set to "default", will use the name of the samples as the labels. If set to "none", no label will be plotted.

Value

a ggplot of the reduced dimension plot of coldata.

Examples

data("mouseBrainSubsetSCE")
plotSCEDimReduceColData(
  inSCE = mouseBrainSubsetSCE, colorBy = "tissue",
  shape = NULL, conditionClass = "factor",
  reducedDimName = "TSNE_counts",
  xlab = "tSNE1", ylab = "tSNE2", labelClusters = TRUE
)


plotSCEDimReduceColData(
  inSCE = mouseBrainSubsetSCE, colorBy = "age",
  shape = NULL, conditionClass = "numeric",
  reducedDimName = "TSNE_counts", bin = c(-Inf, 20, 25, +Inf),
  xlab = "tSNE1", ylab = "tSNE2", labelClusters = FALSE
)